The future operations of one of WA's biggest live export companies were under a cloud last night after Federal authorities found it again breached animal welfare rules.

One of the findings against Livestock Shipping Services handed down yesterday involves shocking footage of cattle having their eyes gouged and legs shot out from under them in Gaza.

Department of Agriculture investigators found LSS committed one minor and two major breaches of export laws over incidents involving sheep and cattle in Gaza and the United Arab Emirates.

Two months ago, the company was hit with a critical non-compliance ruling over incidents in Jordan. That came on top of a major non-compliance finding 12 months ago and the heat-related deaths of more than 4000 sheep LSS exported on a voyage to the Middle East in September.

Federal laws require DoA officials to consider the LSS track record when it next applies for a permit to export animals.

Speaking after the findings against LSS in May, DoA deputy secretary Phillip Glyde would not rule out cancelling export licences if breaches of laws to protect animal welfare continued.

DoA stopped approving cattle exports to Gaza in November but Australian cattle still flow into the war-torn area from Israel.

Lisa Chalk, of Animals Australia, said the findings that nine cattle were outside approved facilities did not reflect the scale of abuse. "All cattle exported to Gaza, numbering in the thousands, have met horrendously cruel deaths," she said.

Australian Livestock Exporters Council chief Alison Penfold said all members were expected to comply with regulations.